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Chowdhury MA, Collins JM, Gell DA, Perry S, Breadmore MC, Shigdar S, King AE. Isolation and Identification of the High-Affinity DNA Aptamer Target to the Brain-Derived Neurotrophic Factor (BDNF). ACS Chem Neurosci 2024; 15:346-356. [PMID: 38149631 DOI: 10.1021/acschemneuro.3c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Aptamers are functional oligonucleotide ligands used for the molecular recognition of various targets. The natural characteristics of aptamers make them an excellent alternative to antibodies in diagnostics, therapeutics, and biosensing. DNA aptamers are mainly single-stranded oligonucleotides (ssDNA) that possess a definite binding to targets. However, the application of aptamers to the fields of brain health and neurodegenerative diseases has been limited to date. Herein, a DNA aptamer against the brain-derived neurotrophic factor (BDNF) protein was obtained by in vitro selection. BDNF is a potential biomarker of brain health and neurodegenerative diseases and has functions in the synaptic plasticity and survival of neurons. We identified eight aptamers that have binding affinity for BDNF from a 50-nucleotide library. Among these aptamers, NV_B12 showed the highest sensitivity and selectivity for detecting BDNF. In an aptamer-linked immobilized sorbent assay (ALISA), the NV_B12 aptamer strongly bound to BDNF protein, in a dose-dependent manner. The dissociation constant (Kd) for NV_B12 was 0.5 nM (95% CI: 0.4-0.6 nM). These findings suggest that BDNF-specific aptamers could be used as an alternative to antibodies in diagnostic and detection assays for BDNF.
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Affiliation(s)
- Md Anisuzzaman Chowdhury
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Jessica M Collins
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - David A Gell
- Menzies Research Institute, School of Medicine, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
| | - Michael C Breadmore
- Australian Centre for Research on Separation Science (ACROSS), School of Chemistry, University of Tasmania, Sandy Bay, Hobart, Tasmania 7001, Australia
| | - Sarah Shigdar
- School of Medicine, Faculty of Health, Deakin University, Geelong, Victoria 3220, Australia
| | - Anna E King
- Wicking Dementia Research and Education Centre, University of Tasmania, 17 Liverpool Street, Hobart, Tasmania 7000, Australia
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A dual-recognition-controlled electrochemical biosensor for selective and ultrasensitive detection of acrylamide in heat-treated carbohydrate-rich food. Food Chem 2023; 413:135666. [PMID: 36796261 DOI: 10.1016/j.foodchem.2023.135666] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
A synergistic hybrid was fabricated for the electrochemical aptasensing of acrylamide (AAM) via molecularly imprinted technology. The aptasensor depends on the modification of glassy carbon electrode with AuNPs and reduced graphene oxide (rGO)/multiwalled carbon nanotubes (MWCNTs) {Au@rGO-MWCNTs/GCE}. The aptamer (Apt-SH) and AAM (template) were incubated with the electrode. After that, the monomer was electro-polymerized to fabricate molecular imprinted polymeric film (MIP) over the surface of Apt-SH/Au@rGO/MWCNTs/GCE. The modified electrodes were characterized using different morphological and electrochemical techniques. Under optimum conditions, the aptasensor exhibited a linear relationship between AAM concentration and anodic peak current difference (ΔIpa) in the range of 1-600 nM with a limit of quantitation (LOQ, S/N = 10) and a limit of detection (LOD, S/N = 3) of 0.346 and 0.104 nM, respectively. The aptasensor was successfully applied for the determination of AAM in potato fries samples with recoveries % in the range of 98.7-103.4 % and RSDs did not exceed 3.2 %. The advantages of MIP/Apt-SH/Au@rGO/MWCNTs/GCE are low detection limit, high selectivity, and satisfactory stability towards AAM detection.
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Recent developments in application of nucleic acid aptamer in food safety. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Hu Q, Hu S, Li S, Liu S, Liang Y, Cao X, Luo Y, Xu W, Wang H, Wan J, Feng W, Niu L. Boronate Affinity-Based Electrochemical Aptasensor for Point-of-Care Glycoprotein Detection. Anal Chem 2022; 94:10206-10212. [DOI: 10.1021/acs.analchem.2c01699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Qiong Hu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Shuhan Hu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Shiqi Li
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Sijie Liu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yiyi Liang
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Xiaojing Cao
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yilin Luo
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Wanjing Xu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Haocheng Wang
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Jianwen Wan
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Wenxing Feng
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Li Niu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
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Víšová I, Houska M, Vaisocherová-Lísalová H. Biorecognition antifouling coatings in complex biological fluids: a review of functionalization aspects. Analyst 2022; 147:2597-2614. [PMID: 35621143 DOI: 10.1039/d2an00436d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent progress in biointerface research has highlighted the role of antifouling functionalizable coatings in the development of advanced biosensors for point-of-care bioanalytical and biomedical applications dealing with real-world complex samples. The resistance to nonspecific adsorption promotes the biorecognition performance and overall increases the reliability and specificity of the analysis. However, the process of modification with biorecognition elements (so-called functionalization) may influence the resulting antifouling properties. The extent of these effects concerning both functionalization procedures potentially changing the surface architecture and properties, and the physicochemical properties of anchored biorecognition elements, remains unclear and has not been summarized in the literature yet. This critical review summarizes these key functionalization aspects with respect to diverse antifouling architectures showing low or ultra-low fouling quantitative characteristics in complex biological media such as bodily fluids or raw food samples. The subsequent discussion focuses on the impact of functionalization on fouling resistance. Furthermore, this review discusses some of the drawbacks of available surface sensitive characterization methods and highlights the importance of suitable assessment of the resistance to fouling.
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Affiliation(s)
- Ivana Víšová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Prague 8, Czech Republic.
| | - Milan Houska
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Prague 8, Czech Republic.
| | - Hana Vaisocherová-Lísalová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 21 Prague 8, Czech Republic.
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Xue X, Cao X, Wan L, Tong Y, Li T, Xie Y. Cross‐linked network solid polymer electrolyte with self‐healing and high stability for lithium metal battery. POLYM INT 2022. [DOI: 10.1002/pi.6400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xiaoyuan Xue
- School of Environmental and Chemical Engineering, Nanchang Hangkong University, 696 Fenghe South Avenue Nanchang 330063 China
| | - Xiaoyan Cao
- School of Environmental and Chemical Engineering, Nanchang Hangkong University, 696 Fenghe South Avenue Nanchang 330063 China
| | - Long Wan
- School of Environmental and Chemical Engineering, Nanchang Hangkong University, 696 Fenghe South Avenue Nanchang 330063 China
| | - Yongfen Tong
- School of Environmental and Chemical Engineering, Nanchang Hangkong University, 696 Fenghe South Avenue Nanchang 330063 China
| | - Tingting Li
- School of Environmental and Chemical Engineering, Nanchang Hangkong University, 696 Fenghe South Avenue Nanchang 330063 China
| | - Yu Xie
- School of Environmental and Chemical Engineering, Nanchang Hangkong University, 696 Fenghe South Avenue Nanchang 330063 China
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Peng P, Liu C, Li Z, Xue Z, Mao P, Hu J, Xu F, Yao C, You M. Emerging ELISA Derived Technologies for in vitro Diagnostics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Jia W, Xie D, Li F, Wu X, Wang R, Yang L, Liu L, Yin W, Chang S. Evaluation the effect of nanoparticles on the structure of aptamers by analyzing the recognition dynamics of aptamer functionalized nanoparticles. Anal Chim Acta 2021; 1183:338976. [PMID: 34627520 DOI: 10.1016/j.aca.2021.338976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/20/2021] [Indexed: 01/31/2023]
Abstract
Aptamer-functionalized nanoparticles have been widely studied as targeted probes in biomedical applications for targeted therapy and imaging. The rigidity of the nanoparticle could stabilized the spatial structure of the aptamer, ensuring the selectivity and affinity for target recognition in the complex environment. The main aim of this article study was to explore the effect of the spatial structure of aptamer in the interaction between aptamer nanoprobes and receptors. We designed and synthesized aptamer functionalized nanoparticle systems with different derivation lengths, and developed a unique kinetic analysis to quantify affinity interactions. The system used silver decahedral nanoparticles (Ag10NPs), which was then chemically functionalized with thrombin (or IgE) aptamers of different tail lengths to produced different nanoprobes, and employed thrombin (or IgE) as target on a surface plasmon resonance (SPR) biosensor to evaluate the binding of these nanoprobes. Kinetic analysis of the SPR binding curve was performed to evaluated the affinity between nanoprobes and targets. Under the premise of eliminating multivalent interactions, we found that the distance between aptamer and nanoparticle could affect the affinity between nanoprobe and target. Furthermore, we found that keeping a certain distance between aptamer and nanoparticle could effectively improved the recognition efficiency of the aptamer nanoprobe and target. It shows that the rigidity of nanomaterials could maintain the spatial structure of the aptamer.
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Affiliation(s)
- Wenchao Jia
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China.
| | - Danping Xie
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China.
| | - Fangfang Li
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Xiangzong Wu
- Ocean College, Minjiang University, Fuzhou, 350108, China
| | - Rui Wang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Leifeng Yang
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Lijun Liu
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Wenhua Yin
- State Environmental Protection Key Laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, 510655, China
| | - Sheng Chang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory of Drinking Water Source Protection, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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Montserrat Pagès A, Safdar S, Ven K, Lammertyn J, Spasic D. DNA-only bioassay for simultaneous detection of proteins and nucleic acids. Anal Bioanal Chem 2021; 413:4925-4937. [PMID: 34184101 PMCID: PMC8238030 DOI: 10.1007/s00216-021-03458-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/26/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023]
Abstract
Testing multiple biomarkers, as opposed to one, has become a preferred approach for diagnosing many heterogeneous diseases, such as cancer and infectious diseases. However, numerous technologies, including gold standard ELISA and PCR, can detect only one type of biomarker, either protein or nucleic acid (NA), respectively. In this work, we report for the first time simultaneous detection of proteins and NAs in the same solution, using solely functional NA (FNA) molecules. In particular, we combined the thrombin binding aptamer (TBA) and the 10-23 RNA-cleaving DNA enzyme (DNAzyme) in a single aptazyme molecule (Aptazyme1.15-3'), followed by extensive optimization of buffer composition, sequences and component ratios, to establish a competitive bioassay. Subsequently, to establish a multiplex bioassay, we designed a new aptazyme (Aptazyme2.20-5') by replacing the target recognition and substrate sequences within Aptazyme1.15-3'. This designing process included an in silico study, revealing the impact of the target recognition sequence on the aptazyme secondary structure and its catalytic activity. After proving the functionality of the new aptazyme in a singleplex bioassay, we demonstrated the capability of the two aptazymes to simultaneously detect thrombin and NA target, or two NA targets in a multiplex bioassay. High specificity in target detection was achieved with the limits of detection in the low nanomolar range, comparable to the singleplex bioassays. The presented results deepen the barely explored features of FNA for diagnosing multiple targets of different origins, adding an extra functionality to their catalogue.
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Affiliation(s)
- Aida Montserrat Pagès
- Department of Biosystems, Biosensors Group, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium.
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven - University of Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
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Aschl T, Frison G, Moraillon A, Ozanam F, Allongue P, Gouget-Laemmel AC. Insights into the Ochratoxin A/Aptamer Interactions on a Functionalized Silicon Surface by Fourier Transform Infrared and UV-Vis Studies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13908-13917. [PMID: 33166140 DOI: 10.1021/acs.langmuir.0c02358] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The association of a mycotoxin-ochratoxin A (OTA)-with a high-affinity DNA aptamer (anti-OTA) immobilized on a functionalized surface has been investigated at the molecular level. Anti-OTA aptamers are coupled by aminolysis in several steps on an acid-terminated alkyl monolayer grafted on a silicon substrate, and Fourier transform infrared spectroscopy in attenuated total reflection geometry is used to assess the immobilization of anti-OTA (in its unfolded single-strand form) and determine its areal density (ca. 1.4/nm2). IR spectra further demonstrate that the OTA/anti-OTA association is efficient and selective and that several association/dissociation cycles may be conducted on the same surface. The areal density of OTA measured after association on the surface (IR spectroscopy) and after dissociation from the surface (UV-vis spectroscopy) falls in the range 0.16-0.3/nm2 which is close to the areal density of a closed-packed monolayer of anti-OTA aptamers folded to form their G-quadruplex structure. The interactions between OTA and its aptamer at the surface are discussed with the help of density functional theory calculations-to identify the complex IR vibrational modes of OTA in solution-and UV-vis spectroscopy-to determine the protonation state of the adsorbing species (i.e., OTA dissolved in the buffer solution).
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Affiliation(s)
- Timothy Aschl
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, 91128 Palaiseau, France
| | - Gilles Frison
- Laboratoire de Chimie Moléculaire, Ecole Polytechnique, CNRS, IP Paris, 91128 Palaiseau, France
- Laboratoire de Chimie Théorique, Sorbonne Université and CNRS, F-75005 Paris, France
| | - Anne Moraillon
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, 91128 Palaiseau, France
| | - François Ozanam
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, 91128 Palaiseau, France
| | - Philippe Allongue
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, 91128 Palaiseau, France
| | - Anne Chantal Gouget-Laemmel
- Laboratoire de Physique de la Matière Condensée, Ecole Polytechnique, CNRS, IP Paris, 91128 Palaiseau, France
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Sajed S, Kolahdouz M, Sadeghi MA, Razavi SF. High-Performance Estimation of Lead Ion Concentration Using Smartphone-Based Colorimetric Analysis and a Machine Learning Approach. ACS OMEGA 2020; 5:27675-27684. [PMID: 33134731 PMCID: PMC7594326 DOI: 10.1021/acsomega.0c04255] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/05/2020] [Indexed: 05/27/2023]
Abstract
Traditional methods for detection of lead ions in water samples are costly and time-consuming. In this work, an accurate smartphone-based colorimetric sensor was developed utilizing a novel machine learning algorithm. In the presence of Pb2+ ions in the solution of specifically functionalized gold nanoparticles, the color of solution turns from red to purple. Indeed, the color variation of the solution is proportional to Pb2+ concentration. The smartphone camera captures the corresponding color change, and the image is processed by an efficient artificial intelligence protocol. The nonlinear regression approach was used for concentration estimation, in which the parameters of the proposed model are obtained using a new feature extraction algorithm. In prediction of Pb2+ concentration, the average absolute error and root-mean-square error were 0.094 and 0.124, respectively. The influence of pH of the medium, temperature, oligonucleotide concentration, and reaction time on the performance of the proposed sensor was carefully investigated and understood to achieve the best sensor response. This novel sensor exhibited good linearity for the detection of Pb2+ in the concentration range of 0.5-2000 ppb with a detection limit of 0.5 ppb.
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Alkahtani SA. Silver nanoparticles conjugated MnFe-based Prussian blue analogue for voltammetric and impedimetric bioaptasensing of amifostine (ethyol). Mikrochim Acta 2020; 187:576. [PMID: 32975672 DOI: 10.1007/s00604-020-04557-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/13/2020] [Indexed: 11/25/2022]
Abstract
A novel bioaptasensing-based electrochemical method for determination of amifostine (AMF) is proposed. The electrochemical aptasensor is based on modification of a glassy carbon electrode with a nanocomposite consisting of silver nanoparticles @ MnFe Prussian blue analogue nanospheres (AgNPs@MnFePBA NS), followed by immobilization of aptamer via Ag-N bonds (aptamer/AgNPs@MnFePBA NS/GCE). Experimental parameters including pH, incubation time, and aptamer concentrations were optimized. Electrochemical impedance spectroscopy (EIS) and differential pulse voltammetric (DPV) techniques were utilized to quantify AMF. The anodic peak current (∆Ipa) and charge transfer resistance (∆Rct) differences increase in the presence of AMF. Under the optimal conditions, using the redox probe, the electrochemical aptasensor exhibited linear ranges of 0.34-45 nmol L-1 and 0.69-45 nmol L-1 with LODs of 0.11 nmol L-1 and 0.23 nmol L-1 for EIS and DPV, respectively. The aptasensor was used to determine AMF in human plasma and in the presence of interfering species with recoveries and RSDs in the range 97.8-103.2% and 2.2-4.2%, respectively. Graphical abstract.
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Affiliation(s)
- Saad A Alkahtani
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, Kingdom of Saudi Arabia.
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Agrawal DK, Schulman R. Modular protein-oligonucleotide signal exchange. Nucleic Acids Res 2020; 48:6431-6444. [PMID: 32442276 PMCID: PMC7337525 DOI: 10.1093/nar/gkaa405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/02/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.
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Affiliation(s)
- Deepak K Agrawal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.,Department of Bioengineering, University of Colorado Medicine, Aurora, CO 80045, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.,Department of Chemistry, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, 3400 N Charles St, Baltimore, Maryland 21218, USA
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El-Wekil MM, Darweesh M, Shaykoon MSA, Ali R. Enzyme-free and label-free strategy for electrochemical oxaliplatin aptasensing by using rGO/MWCNTs loaded with AuPd nanoparticles as signal probes and electro-catalytic enhancers. Talanta 2020; 217:121084. [DOI: 10.1016/j.talanta.2020.121084] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022]
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Mahmoud AM, Alkahtani SA, Alyami BA, El-Wekil MM. Dual-recognition molecularly imprinted aptasensor based on gold nanoparticles decorated carboxylated carbon nanotubes for highly selective and sensitive determination of histamine in different matrices. Anal Chim Acta 2020; 1133:58-65. [PMID: 32993874 DOI: 10.1016/j.aca.2020.08.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 12/31/2022]
Abstract
In this study, an electrochemical aptamer based sensor (aptasensor) was proposed for specific recognition of histamine (HIS). The electrochemical aptasensor based on fabrication of glassy carbon electrode (GCE) with molecular imprinted polymer (MIP) and DNA aptamers on gold nanoparticles (AuNPs) and carboxylated carbon nanotubes (cCNTs) (MIP-apta/AuNPs/cCNTs/GCE). The aptasensor exhibits high selectivity towards HIS detection as it has two recognition elements which are MIP cavities and aptamer interaction. Upon exposure of MIP-apt/AuNPs/cCNTs/GCE to HIS, the current of redox probe was decreased that depends on the template (HIS) concentration. The effects of aptamer concentration, incubation time, pH and AuNPs electro-deposition time were optimized. Differential pulse voltammetry (DPV) and electrochemical impedance spectroscopy (EIS) techniques were used to analyze HIS in complicated matrices. Favorable performance of MIP-apt/AuNPs/cCNTs/GCE was achieved with linearity ranges of 0.46-35 nmol L-1 and 0.35-35 nmol L-1 with limits of detection (LODs, S/N = 3) of 0.15 nmol L-1 and 0.11 nmol L-1 using DPV and EIS, respectively. The fabricated aptasensor displayed high selectivity, desirable reproducibility and stability. The MIP-apt/AuNPs/cCNTs/GCE was used to detect HIS in human plasma and canned tuna samples with good recoveries % and RSDs %.
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Affiliation(s)
- Ashraf M Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Najran University, Najran, Saudi Arabia; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt
| | - Saad A Alkahtani
- Department of Clinical Pharmacy, College of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Bandar A Alyami
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Najran University, Najran, Saudi Arabia
| | - Mohamed M El-Wekil
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Assiut University, Assiut, Egypt.
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Fellows T, Ho L, Flanagan S, Fogel R, Ojo D, Limson J. Gold nanoparticle-streptavidin conjugates for rapid and efficient screening of aptamer function in lateral flow sensors using novel CD4-binding aptamers identified through Crossover-SELEX. Analyst 2020; 145:5180-5193. [PMID: 32567629 DOI: 10.1039/d0an00634c] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To decrease the burden of laborious and reagent-intensive screening of modified aptamers, their binding function requires assessment in assay formats compatible with the end diagnostic application. Here, we report on the use of an alternative and cost-effective approach: a rapid lateral flow assay (LFA) utilising streptavidin-conjugated gold nanoparticles (AuNP) as reporter molecules to screen novel ssDNA aptamers for their ability to detect CD4. Crossover-SELEX was employed to identify CD4-targeting aptamers from a ssDNA library enriched against a recombinant human CD4 protein (hCD4) conjugated to magnetic-beads and to endogenous CD4 expressed by U937 cells. Counter-selection with IgG-conjugated beads and CD4-negative Ramos RA-1 cells was employed. Following SELEX, four sequences (U4, U14, U20 and U26) were selected for candidate screening. Fluorescence confocal microscopy showed comparable localization of the Cy5-labeled aptamer U26, compared to antibodies binding CD4's cytoplasmic domain. Aptamer-hCD4 binding kinetics were evaluated by a qPCR-based magnetic-bead binding assay to unmodified aptamers. U26 exhibited the highest binding affinity (Kd = 2.93 ± 1.03 nM) to hCD4-conjugated beads. Citrate-stabilized gold nanoparticles (mean particle diameter, 10.59 ± 1.81 nm) were functionalized with streptavidin to allow immobilization of biotin-labeled aptamers. Except for U4, the aptamer-gold nanoparticle conjugates (Apt-AuNP) remained stable under physiological conditions with their size (approx. 15 nm) appropriate for use in the LFAs. Lateral-flow based screening was used to evaluate the suitability of the Apt-AuNPs as CD4-detecting reporter molecules by immobilizing hCD4 and flowing the nanoparticle conjugates across the LFA. Using this approach, two novel sequences were identified as being suitable for the detection of hCD4: visual detection at 9 min was obtained using U20 or U26. After 20 min, equivalent colorimetric hCD4 responses were observed between anti-CD4 monoclonal antibody (ΔI = 94.19 ± 3.71), an existing CD4 aptamer F1-62 (ΔI = 90.31 ± 19.31) and U26 (ΔI = 100.14 ± 14.61) LFA's, each demonstrating high specificity to hCD4 compared to IgG. From the above, Crossover-SELEX allowed for the successful identification of ssDNA aptamers able to detect hCD4. Streptavidin-conjugated AuNPs, when bound to candidate aptamers, show potential application here as screening tools for the rapid evaluation of aptamer performance in low-cost lateral flow diagnostics.
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Affiliation(s)
- Tamika Fellows
- Rhodes University Biotechnology Innovation Centre, Grahamstown, Eastern Cape, South Africa.
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17
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Miyagawa A, Okada Y, Okada T. Aptamer-Based Sensing of Small Organic Molecules by Measuring Levitation Coordinate of Single Microsphere in Combined Acoustic-Gravitational Field. ACS OMEGA 2020; 5:3542-3549. [PMID: 32118169 PMCID: PMC7045491 DOI: 10.1021/acsomega.9b03860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
We present aptamer-based sensing using a coupled acoustic-gravitational (CAG) field, which transduces a change in the density of a microparticle (MP) to a change in the levitation coordinate. A large density of the MP is initially induced by the binding of gold nanoparticles (AuNPs) on the MP through sandwich hybridization with aptamer DNA molecules. Targets added to the system interact with the aptamer DNA molecules to form complexes, and the duplex between the aptamer and the probe DNA molecules is dissociated. This leads to the release of AuNPs from the MP and a decrease in its density. As the target concentration increases, the levitation coordinate of the MP increases. From the levitation coordinate shift, we can determine the target concentration. The detection limits for adenosine triphosphate, dopamine, and ampicillin as test targets are 9.8 nM, 17 nM, and 160 pM, respectively. The dissociation constants for the aptamer-target complexes are quantitatively determined from the dependence of the levitation coordinate on the target concentration. This scheme is a useful analytical tool not only for the trace analyses of targets but also for the evaluation of aptamer-target interactions.
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18
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Zhao L, Fu J, Du Z, Jia X, Qu Y, Yu F, Du J, Chen Y. High-strength and flexible cellulose/PEG based gel polymer electrolyte with high performance for lithium ion batteries. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2019.117428] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Martín-Gracia B, Martín-Barreiro A, Cuestas-Ayllón C, Grazú V, Line A, Llorente A, M. de la Fuente J, Moros M. Nanoparticle-based biosensors for detection of extracellular vesicles in liquid biopsies. J Mater Chem B 2020; 8:6710-6738. [DOI: 10.1039/d0tb00861c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Selecting the appropriate nanoparticle, functionalization chemistry and sensing methodology can speed up the translation of liquid biopsies into the clinic.
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Affiliation(s)
- Beatriz Martín-Gracia
- Aragón Materials Science Institute (ICMA)
- CSIC/University of Zaragoza
- Zaragoza
- Spain
- Biomedical Research Networking Center in Bioengineering
| | - Alba Martín-Barreiro
- Aragón Materials Science Institute (ICMA)
- CSIC/University of Zaragoza
- Zaragoza
- Spain
- Biomedical Research Networking Center in Bioengineering
| | | | - Valeria Grazú
- Aragón Materials Science Institute (ICMA)
- CSIC/University of Zaragoza
- Zaragoza
- Spain
- Biomedical Research Networking Center in Bioengineering
| | - Aija Line
- Latvian Biomedical Research and Study Centre
- Riga
- Latvia
| | - Alicia Llorente
- Department of Molecular Cell Biology
- Institute for Cancer Research
- Oslo University Hospital
- Oslo
- Norway
| | - Jesús M. de la Fuente
- Aragón Materials Science Institute (ICMA)
- CSIC/University of Zaragoza
- Zaragoza
- Spain
- Biomedical Research Networking Center in Bioengineering
| | - María Moros
- Aragón Materials Science Institute (ICMA)
- CSIC/University of Zaragoza
- Zaragoza
- Spain
- Biomedical Research Networking Center in Bioengineering
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20
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Casanova-Morales N, Figueroa NL, Alfaro K, Montenegro F, Barrera NP, Maze JR, Wilson CAM, Conejeros P. Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations. PLoS One 2019; 14:e0222468. [PMID: 31697710 PMCID: PMC6837747 DOI: 10.1371/journal.pone.0222468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/30/2019] [Indexed: 02/07/2023] Open
Abstract
Optical tweezers have enabled the exploration of picoNewton forces and dynamics in single-molecule systems such as DNA and molecular motors. In this work, we used optical tweezers to study the folding/unfolding dynamics of the APTSTX1-aptamer, a single-stranded DNA molecule with high affinity for saxitoxin (STX), a lethal neurotoxin. By measuring the transition force during (un)folding processes, we were able to characterize and distinguish the conformational changes of this aptamer in the presence of magnesium ions and toxin. This work was supported by molecular dynamics (MD) simulations to propose an unfolding mechanism of the aptamer-Mg+2 complex. Our results are a step towards the development of new aptamer-based STX sensors that are potentially cheaper and more sensitive than current alternatives.
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Affiliation(s)
- Nathalie Casanova-Morales
- Instituto de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
- Facultad de Artes Liberales, Universidad Adolfo Ibáñez, Santiago, Chile
| | | | - Karol Alfaro
- CIGREN. Instituto de Biología. Facultad de Ciencias. Universidad de Valparaíso, Valparaíso, Chile
| | - Felipe Montenegro
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nelson P. Barrera
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - J. R. Maze
- Instituto de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Christian A. M. Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Pablo Conejeros
- CIGREN. Instituto de Biología. Facultad de Ciencias. Universidad de Valparaíso, Valparaíso, Chile
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21
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Kurseev SA, Solovjev AM, Neumann MM, Medvedko AV, Sakharov IY. Chemiluminescent and Colorimetric Aptamer-Based Assays of Human α-Thrombin. ANAL LETT 2019. [DOI: 10.1080/00032719.2019.1640718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Sergei A. Kurseev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Anton M. Solovjev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Marina M. Neumann
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | | | - Ivan Yu. Sakharov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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22
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An electrochemical aptasensor for highly sensitive detection of zearalenone based on PEI-MoS2-MWCNTs nanocomposite for signal enhancement. Anal Chim Acta 2019; 1060:71-78. [DOI: 10.1016/j.aca.2019.02.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 01/29/2019] [Accepted: 02/08/2019] [Indexed: 11/17/2022]
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23
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Jung Y, Lee CY, Park KS, Park HG. Sensitive and specific detection of proteins based on target-responsive DNA polymerase activity. Anal Chim Acta 2019; 1059:80-85. [PMID: 30876635 DOI: 10.1016/j.aca.2019.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 11/09/2018] [Accepted: 01/15/2019] [Indexed: 10/27/2022]
Abstract
We herein describe a novel method for the detection of target protein based on the target-responsive DNA polymerase activity. In the sensor, two different types of DNA aptamers with the respective functions: one binds to the target protein and the other binds to DNA polymerase, are rationally engineered and combined to form the detection probe that regulates DNA polymerase activity in response to the target protein. In the presence of target protein, the detection probe becomes destabilized and stops the inhibition of DNA polymerase activity. Consequently, the active DNA polymerase initiates the primer extension reaction on the target-specific DNA aptamer, which recycles the target protein to promote another activation cycle of DNA polymerase. In addition, DNA polymerase also catalyzes the primer extension reaction on the primer/template complex in conjugation with TaqMan probe, leading to the significantly enhanced fluorescence intensities. With this novel strategy, we detected a model target protein, lysozyme with a limit of detection as low as 0.80 nM. In addition, the practical applicability of this system was successfully demonstrated by determining lysozyme in human serum.
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Affiliation(s)
- Yujin Jung
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21+ Program), KAIST, Daehak-ro 291, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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24
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Yarahmadi S, Azadbakht A, Derikvand RM. Hybrid synthetic receptor composed of molecularly imprinted polydopamine and aptamers for impedimetric biosensing of urea. Mikrochim Acta 2019; 186:71. [PMID: 30627876 DOI: 10.1007/s00604-018-3180-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
An electrochemical aptamer-based method is described for highly specific sensing of urea. Urea-imprinted polydopamine was obtained by electropolymerization of dopamine (DA). The molecularly imprinted polymer (MIP) also contains DNA aptamers on gold nanoparticles decorated with a carbon nanotube network (AuNP/CNT). The material was placed on a glassy carbon electrode (GCE). After removal of urea from the MIP cavities, the GCE display double recognition capability which makes it superior to conventional MIP-only or aptamer-only based assays. On exposure of the modified electrode to urea, the interfacial charge transfer of the redox probe hexacyanoferrate is traced, typically measured at a peak voltage of 0.22 V vs. Ag/AgCl. The change in charge transfer resistance depends on the urea concentration. The assay has a 900 fM detection limit, and response is the linear up to 500 nM urea concentrations. Graphical abstract ᅟ.
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Affiliation(s)
- Saeed Yarahmadi
- Department of Chemistry, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Azadeh Azadbakht
- Department of Chemistry, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran.
| | - Reza Mir Derikvand
- Department of Plant Breeding, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
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25
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An aptamer embedded in a molecularly imprinted polymer for impedimetric determination of tetracycline. Mikrochim Acta 2019; 186:56. [PMID: 30617424 DOI: 10.1007/s00604-018-3123-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
The authors introduce a new kind of aptameric imprinted polymer for sensing tetracycline (TET), thereby combining the unique features of aptamer-based and molecularly imprinted polymer based recognition. The dual recognition scheme results in sensing capabilities that are superior to those of the aptamer alone, or of a conventional molecularly imprinted polymer alone. In the first step, the aptamer-TET complex was immobilized on the surface of a glassy carbon electrode (GCE) decorated with gold nanoparticles. Dopamine was then electropolymerized on the surface of the modified GCE to entrap the aptamer-TET complex. TET was then extracted with an ethanol-acetic acid mixture (95:5) in order to create void cavities. On exposure to TET, the cavities are filled with TET again, and this leads to a retardment of the interfacial charge transfer of the redox probe hexacyanoferrate, typically measured at a peak voltage of 0.22 V vs. Ag/AgCl. The assay detects TET in the concentration ranges from 0.5-100 pM and from 1-1000 nM with a very low limit of detection of 144 fM. Its superior selectivity and affinity make this assay a viable tool as demonstrated for the successful analysis of TET in spiked milk samples. Graphical abstract Schematic representation of a glassy carbon electrode (GCE) modified with gold nanoparticles (AuNPs) and coated with an aptamer-imprinted polymer (MIP).
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26
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Geldert A, Kenry, Zhang X, Zhang H, Lim CT. Enhancing the sensing specificity of a MoS 2 nanosheet-based FRET aptasensor using a surface blocking strategy. Analyst 2018; 142:2570-2577. [PMID: 28569315 DOI: 10.1039/c7an00640c] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aptamer-based biosensing, which uses short, single-stranded nucleic acid segments to bind to a target, can be advantageous over antibody-based diagnostics due to the ease of synthesis and high stability of aptamers. However, the development of most aptamer-based sensors (aptasensors) is still in its initial stages and many factors affecting their performance have not been studied in great detail. Here, we enhance the sensing specificity of a fluorescence resonance energy transfer (FRET)-based MoS2 nanosheet aptasensor in detecting the malarial biomarker Plasmodium lactate dehydrogenase (pLDH). In this sensing scheme, the presence of target is signaled by an increase in fluorescence when fluorescently-labeled aptamers bind to pLDH and release from a quenching material. Interestingly, unlike most of the reported literature on aptasensors, we observe that non-target proteins also cause a considerable increase in the detected fluorescence. This may be due to the nonspecific adsorption of proteins onto the fluorescence quencher, leading to the displacement of aptamers from the quencher surface. To reduce this nonspecific association and to enhance the sensor specificity, we propose the application of a surface blocking agent to the quenching material. Importantly, we demonstrate that the sensing specificity of the MoS2 nanosheet-based aptasensor towards target pLDH biomolecules can be significantly enhanced through surface passivation, thus contributing to the development of highly selective and robust point-of-care malaria diagnostics.
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Affiliation(s)
- Alisha Geldert
- Department of Biomedical Engineering, National University of Singapore, Singapore 117576.
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27
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Cao HX, Wang L, Pan CG, He YS, Liang GX. Aptamer based electrochemiluminescent determination of bisphenol A by using carboxylated graphitic carbon nitride. Mikrochim Acta 2018; 185:463. [PMID: 30225568 DOI: 10.1007/s00604-018-2997-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/08/2018] [Indexed: 12/14/2022]
Abstract
An electrochemiluminescence (ECL) based assay is described for the determination of the endocrine disruptor bisphenol A (BPA). The method is based on the use of carboxylated graphitic carbon nitride (C-g-C3N4) carrying an immobilized aptamer against BPA. In the presence of BPA, the ECL signal decreases due to ECL energy transfer from excited-state C-g-C3N4 to the BPA oxidation product. Under the optimal conditions, ECL intensity increases linearly in the 0.1 pM to 1 nM BPA concentration range. The detection limit is as low as 30 fM. The assay has excellent sensitivity, outstanding stability and high selectivity. It was applied to the determination of BPA in spiked water samples. Graphical abstract Aptamer modified carboxylated graphitic carbon nitride was synthesized and applied in an electrochemiluminescence-based aptasensor for bisphenol A.
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Affiliation(s)
- Hai-Xia Cao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China
| | - Li Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, China.
| | - Chang-Gang Pan
- School of the Environment, Jiangsu University, Zhenjiang, 212013, China
| | - Yu-Sheng He
- School of the Environment, Jiangsu University, Zhenjiang, 212013, China
| | - Guo-Xi Liang
- School of the Environment, Jiangsu University, Zhenjiang, 212013, China.
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28
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Gating Hysteresis as an Indicator for Silicon Nanowire FET Biosensors. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8060950] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Acquah C, Danquah MK, Chan YW, Moy CKS, Ongkudon CM, Lau SY. Chromatographic characterisation of aptamer-modified poly(EDMA-co-GMA) monolithic disk format for protein binding and separation. SEP SCI TECHNOL 2018. [DOI: 10.1080/01496395.2018.1443139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Caleb Acquah
- Curtin Malaysia Research Institute, Curtin University, Miri, Malaysia
- Department of Chemical Engineering, Curtin University, Miri, Malaysia
| | - Michael K. Danquah
- Curtin Malaysia Research Institute, Curtin University, Miri, Malaysia
- Department of Chemical Engineering, Curtin University, Miri, Malaysia
| | - Yi Wei Chan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Charles K. S. Moy
- Department of Civil Engineering, Xi’an Jiaotong-Liverpool University, Suzhou, China
| | - Clarence M. Ongkudon
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - Sie Yon Lau
- Department of Chemical Engineering, Curtin University, Miri, Malaysia
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A glassy carbon electrode modified with carbon nanotubes and reduced graphene oxide decorated with platinum-gold nanoparticles for voltammetric aptasensing of urea. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2494-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Lietard J, Abou Assi H, Gómez-Pinto I, González C, Somoza MM, Damha MJ. Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays. Nucleic Acids Res 2017; 45:1619-1632. [PMID: 28100695 PMCID: PMC5389548 DOI: 10.1093/nar/gkw1357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/28/2016] [Indexed: 01/13/2023] Open
Abstract
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.,Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | - Hala Abou Assi
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
| | | | - Carlos González
- Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria
| | - Masad J Damha
- Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada
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Zhang J, Loo RRO, Loo JA. Structural Characterization of a Thrombin-Aptamer Complex by High Resolution Native Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1815-1822. [PMID: 28755259 PMCID: PMC5711526 DOI: 10.1007/s13361-017-1751-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Revised: 06/11/2017] [Accepted: 06/30/2017] [Indexed: 05/12/2023]
Abstract
Native mass spectrometry (MS) with electrospray ionization (ESI) has evolved as an invaluable tool for the characterization of intact native proteins and non-covalently bound protein complexes. Here we report the structural characterization by high resolution native top-down MS of human thrombin and its complex with the Bock thrombin binding aptamer (TBA), a 15-nucleotide DNA with high specificity and affinity for thrombin. Accurate mass measurements revealed that the predominant form of native human α-thrombin contains a glycosylation mass of 2205 Da, corresponding to a sialylated symmetric biantennary oligosaccharide structure without fucosylation. Native MS showed that thrombin and TBA predominantly form a 1:1 complex under near physiological conditions (pH 6.8, 200 mM NH4OAc), but the binding stoichiometry is influenced by the solution ionic strength. In 20 mM ammonium acetate solution, up to two TBAs were bound to thrombin, whereas increasing the solution ionic strength destabilized the thrombin-TBA complex and 1 M NH4OAc nearly completely dissociated the complex. This observation is consistent with the mediation of thrombin-aptamer binding through electrostatic interactions and it is further consistent with the human thrombin structure that contains two anion binding sites on the surface. Electron capture dissociation (ECD) top-down MS of the thrombin-TBA complex performed with a high resolution 15 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer showed the primary binding site to be at exosite I located near the N-terminal sequence of the heavy chain, consistent with crystallographic data. High resolution native top-down MS is complementary to traditional structural biology methods for structurally characterizing native proteins and protein-DNA complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Jiang Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA.
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33
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Li S, Liu C, Han B, Luo J, Yin G. An electrochemiluminescence aptasensor switch for aldicarb recognition via ruthenium complex-modified dendrimers on multiwalled carbon nanotubes. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2177-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Chen L, Chao J, Qu X, Zhang H, Zhu D, Su S, Aldalbahi A, Wang L, Pei H. Probing Cellular Molecules with PolyA-Based Engineered Aptamer Nanobeacon. ACS APPLIED MATERIALS & INTERFACES 2017; 9:8014-8020. [PMID: 28221021 DOI: 10.1021/acsami.6b16764] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that is of critical importance in many cellular processes. The development of sensitive and selective methods for the detection of ATP level in vivo is crucial in diagnostic and theranostic applications. In this work, we have developed a polyA-based aptamer nanobeacon (PAaptNB) with improved efficiency and speed of ATP analysis. We found that the dissociation constants and competitive binding kinetics of the PAaptNB could be programmably regulated by adjusting the polyA length. When the polyA length reached to 30 bases, a 10 μM detection limit for ATP assay with PAaptNB can be achieved (∼10-fold improvement compared with the conventional thiol-based aptamer nanobeacon). The feasibility of the PAaptNB for in vivo assay was further demonstrated by imaging intracellular ATP molecules. This study provides a new strategy to construct high-efficiency and high-speed biosensors for cellular molecules analysis, which holds great potential in bioanalysis and theranostic applications.
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Affiliation(s)
- Lizhen Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, PR China
| | - Jie Chao
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, PR China
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Dan Zhu
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Shao Su
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Lianhui Wang
- Institute of Advanced Materials, Nanjing University of Posts and Telecommunications , Nanjing 210023, PR China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, PR China
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Lee DW, Park KM, Gong B, Shetty D, Khedkar JK, Baek K, Kim J, Ryu SH, Kim K. A simple modular aptasensor platform utilizing cucurbit[7]uril and a ferrocene derivative as an ultrastable supramolecular linker. Chem Commun (Camb) 2016; 51:3098-101. [PMID: 25597690 DOI: 10.1039/c4cc08027k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A simple modular aptamer-based sensor (aptasensor) platform was prepared by combining the merits of the rapid and efficient preparation of a self-assembled monolayer of cucurbit[7]uril (CB[7] SAM) and the strong and specific binding affinity of CB[7] to ferrocenemethylammonium (FA), as an ultrastable supramolecular linker, to immobilize aptamers on CB[7] SAM.
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Affiliation(s)
- Don-Wook Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), Pohang, 790-784, Republic of Korea
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Trends in the Design and Development of Specific Aptamers Against Peptides and Proteins. Protein J 2016; 35:81-99. [DOI: 10.1007/s10930-016-9653-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
Convergence of localized surface plasmon resonance of metal nanoparticles with classical ELISA has emerged as a new class of immunoassays, i.e. plasmonic ELISA, enabling biocatalysis mediated ultrasensitive naked-eye detection of disease biomarkers.
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Affiliation(s)
- Jitendra Satija
- School of BioSciences and Technology (SBST)
- VIT University
- Vellore
- India
| | - Nirmal Punjabi
- Department of Biosciences and Bioengineering
- IIT Bombay
- Mumbai 400 076
- India
| | - Debasish Mishra
- School of BioSciences and Technology (SBST)
- VIT University
- Vellore
- India
- Centre for Biomaterials, Cellular and Molecular Theranostics (CBCMT)
| | - Soumyo Mukherji
- Department of Biosciences and Bioengineering
- IIT Bombay
- Mumbai 400 076
- India
- Centre of Excellence for Nanoelectronics
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Terracciano M, De Stefano L, Borbone N, Politi J, Oliviero G, Nici F, Casalino M, Piccialli G, Dardano P, Varra M, Rea I. Solid phase synthesis of a thrombin binding aptamer on macroporous silica for label free optical quantification of thrombin. RSC Adv 2016. [DOI: 10.1039/c6ra18401d] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Human α-thrombin (TB) is a serine protease with a crucial role in coagulation and hemostasis.
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Affiliation(s)
- Monica Terracciano
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Luca De Stefano
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Nicola Borbone
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Jane Politi
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Giorgia Oliviero
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Fabrizia Nici
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Maurizio Casalino
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | | | - Principia Dardano
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
| | - Michela Varra
- Department of Pharmacy
- University of Naples Federico II
- Naples
- Italy
| | - Ilaria Rea
- Institute for Microelectronics and Microsystems
- National Council of Research
- Naples
- Italy
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Wang Q, Luo B, Yang X, Wang K, Liu L, Du S, Li Z. Elucidation of the effect of aptamer immobilization strategies on the interaction between cell and its aptamer using atomic force spectroscopy. J Mol Recognit 2015; 29:151-8. [PMID: 26530526 DOI: 10.1002/jmr.2514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/24/2015] [Accepted: 09/30/2015] [Indexed: 12/13/2022]
Abstract
The immobilization strategy of cell-specific aptamers is of great importance for studying the interaction between a cell and its aptamer. However, because of the difficulty of studying living cell, there have not been any systematic reports about the effect of immobilization strategies on the binding ability of an immobilized aptamer to its target cell. Because atomic force spectroscopy (AFM) could not only be suitable for the investigation of living cell under physiological conditions but also obtains information reflecting the intrinsic properties of individuals, the effect of immobilization strategies on the interaction of aptamer/human hepatocarcinoma cell Bel-7404 was successively evaluated using AFM here. Two different immobilization methods, including polyethylene glycol immobilization method and glutaraldehyde immobilization method were used, and the factors, such as aptamer orientation, oligodeoxythymidine spacers and dodecyl spacers, were investigated. Binding events measured by AFM showed that a similar unbinding force was obtained regardless of the change of the aptamer orientation, the immobilization method, and spacers, implying that the biophysical characteristics of the aptamer at the molecular level remain undisturbed. However, it showed that the immobilization orientation, immobilization method, and spacers could alter the binding probability of aptamer/Bel-7404 cell. Presumably, these factors may affect the accessibility of the aptamer toward its target cell. These results may provide valuable information for aptamer sensor platforms including ultrasensitive biosensor design.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Bianxia Luo
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Lin Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Shasha Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
| | - Zhiping Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, China
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Scarano S, Dausse E, Crispo F, Toulmé JJ, Minunni M. Design of a dual aptamer-based recognition strategy for human matrix metalloproteinase 9 protein by piezoelectric biosensors. Anal Chim Acta 2015; 897:1-9. [DOI: 10.1016/j.aca.2015.07.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 02/07/2023]
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Cai S, Cao Z, Lau C, Lu J. Label-free technology for the amplified detection of microRNA based on the allosteric hairpin DNA switch and hybridization chain reaction. Analyst 2015; 139:6022-7. [PMID: 25270599 DOI: 10.1039/c4an01178c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
By using the allosteric hairpin DNA switch, a novel assay for the detection of microRNA (miRNA) let-7a via a hybridization chain reaction (HCR) was introduced. Briefly, the hairpin DNA switch probe is a single-stranded DNA consisting of a streptavidin (SA) aptamer sequence, a target binding sequence and a certain sequence that acts as a trigger of the HCR. In the presence of target let-7a, the hairpin DNA switch would open and expose the stem region sequences, where a part of this sequence acts as initiator sequence strands for the HCR and triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers, another part is the SA aptamer sequence which activates its binding affinity to SA on SA-coated magnetic particles. The hybridization event could be sensitively detected via an instantaneous derivatization reaction between a special chemiluminescence (CL) reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotides within the target, the hairpin DNA switch probe, and HCR helices to form an unstable CL intermediate for the generation of light. Our results show that the coupling of the hairpin DNA switch probe and the HCR for the amplified detection of let-7a achieves a better performance (e.g. wide linear response range: 0.1-1000 fmol, low detection limit: 0.1 fmol, and high specificity). Furthermore, this approach could be easily applied to the detection of let-7a in human lung cells, and extended to detect other types of miRNA and proteins such as PDGF based on aptamers. We believe such advancements will represent a significant step towards improved diagnostics and more personalized medical treatment.
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Affiliation(s)
- Sheng Cai
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.
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Aptekar S, Arora M, Lawrence CL, Lea RW, Ashton K, Dawson T, Alder JE, Shaw L. Selective Targeting to Glioma with Nucleic Acid Aptamers. PLoS One 2015; 10:e0134957. [PMID: 26252900 PMCID: PMC4529171 DOI: 10.1371/journal.pone.0134957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/16/2015] [Indexed: 12/11/2022] Open
Abstract
Malignant glioma is characterised by a rapid growth rate and high capacity for invasive infiltration to surrounding brain tissue; hence, diagnosis and treatment is difficult and patient survival is poor. Aptamers contribute a promising and unique technology for the in vitro imaging of live cells and tissues, with a potentially bright future in clinical diagnostics and therapeutics for malignant glioma. The binding selectivity, uptake capacity and binding target of two DNA aptamers, SA43 and SA44, were investigated in glioma cells and patient tissues. The binding assay showed that SA43 and SA44 bound with strong affinity (Kd, 21.56 ± 4.60 nM and Kd, 21.11 ± 3.30 nM respectively) to the target U87MG cells. Quantitative analysis by flow cytometry showed that the aptamers were able to actively internalise in U87MG and 1321N1 glioma cells compared to the non-cancerous and non-glioma cell types. Confocal microscopy confirmed staining in the cytoplasm, and co-localisation studies with endoplasmic reticulum, Golgi apparatus and lysosomal markers suggested internalisation and compartmentalisation within the endomembrane system. Both aptamers selectively bound to Ku 70 and Ku 80 DNA repair proteins as determined by aptoprecipitation (AP) followed by mass spectrometry analysis and confirmation by Western blot. In addition, aptohistochemical (AHC) staining on paraffin embedded, formalin fixed patient tissues revealed that the binding selectivity was significantly higher for SA43 aptamer in glioma tissues (grade I, II, III and IV) compared to the non-cancerous tissues, whereas SA44 did not show selectivity towards glioma tissues. The results indicate that SA43 aptamer can differentiate between glioma and non-cancerous cells and tissues and therefore, shows promise for histological diagnosis of glioma.
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Affiliation(s)
- Shraddha Aptekar
- School of Pharmacy and Biomedical Sciences, College of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, United Kingdom
| | - Mohit Arora
- School of Pharmacy and Biomedical Sciences, College of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, United Kingdom
- Department of Neuropathology, Lancashire Teaching Hospitals (NHS trust), Preston, PR2 9HT, United Kingdom
| | - Clare Louise Lawrence
- School of Pharmacy and Biomedical Sciences, College of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, United Kingdom
| | - Robert William Lea
- School of Pharmacy and Biomedical Sciences, College of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, United Kingdom
| | - Katherine Ashton
- Department of Neuropathology, Lancashire Teaching Hospitals (NHS trust), Preston, PR2 9HT, United Kingdom
| | - Tim Dawson
- Department of Neuropathology, Lancashire Teaching Hospitals (NHS trust), Preston, PR2 9HT, United Kingdom
| | - Jane Elizabeth Alder
- School of Pharmacy and Biomedical Sciences, College of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, United Kingdom
| | - Lisa Shaw
- School of Pharmacy and Biomedical Sciences, College of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, United Kingdom
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43
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Zhou W, Huang PJJ, Ding J, Liu J. Aptamer-based biosensors for biomedical diagnostics. Analyst 2015; 139:2627-40. [PMID: 24733714 DOI: 10.1039/c4an00132j] [Citation(s) in RCA: 329] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.
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Affiliation(s)
- Wenhu Zhou
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Central South University, Tongzipo Road #172, Changsha 410013, Hunan, PR China.
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Liu LH, Zhou XH, Shi HC. Portable optical aptasensor for rapid detection of mycotoxin with a reversible ligand-grafted biosensing surface. Biosens Bioelectron 2015; 72:300-5. [PMID: 26000463 DOI: 10.1016/j.bios.2015.05.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/17/2022]
Abstract
As food safety is gaining prominence as a global issue, the demand for developing rapid, simple, on-site, accurate and low-cost biosensor technologies will continue to grow. This study demonstrates an evanescent wave optical aptasensor with a reversible ligand-grafted biosensing surface for rapid, sensitive and highly selective detection of ochratoxin A (OTA) in food. In this system, the OTA molecules were covalently immobilized onto the surface of an optical fiber using glutaraldehyde and ethylenediamine as space linkers. An integrated evanescent wave all-fiber (EWA) biosensing platform was developed for investigating the binding kinetics between the tethered ligand and free OTA-aptamer, the performance of the aptamer-based bioassay and the reversibility of biosensing surface. The affinity constant (Ka) of aptamer with tethered OTA was measured to be 2.2 × 10(8)M(-1) based on the EWA biosensing platform. With a competitive detection mode, the quantification of OTA over concentration ranges from 0.73 μg L(-1) to 12.50 μg L(-1) with a detection limit of 0.39 μg L(-1). The performance of the aptasensor with other interfering mycotoxins and spiked real wheat samples shows high specificity and selectivity, good recovery, precision, and accuracy, indicating that it can be applied for on-site, inexpensive and easy-to-use monitoring of OTA in real samples. Moreover, since the organic ligands are grafted onto the fiber surface, this strategy may avoid the potential disadvantages caused by immobilizing the nucleic acid biomolecules, such as weak restoration to the original DNA conformation after repeated uses.
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Affiliation(s)
- Lan-hua Liu
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiao-hong Zhou
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Han-chang Shi
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
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45
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Chen A, Yang S. Replacing antibodies with aptamers in lateral flow immunoassay. Biosens Bioelectron 2015; 71:230-242. [PMID: 25912679 DOI: 10.1016/j.bios.2015.04.041] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/12/2015] [Accepted: 04/13/2015] [Indexed: 12/30/2022]
Abstract
Aptamers have been identified against various targets as a type of chemical or nucleic acid ligand by systematic evolution of ligands by exponential enrichment (SELEX) with high sensitivity and specificity. Aptamers show remarkable advantages over antibodies due to the nucleic acid nature and target-induced structure-switching properties and are widely used to design various fluorescent, electrochemical, or colorimetric biosensors. However, the practical applications of aptamer-based sensing and diagnostics are still lagging behind those of antibody-based tests. Lateral flow immunoassay (LFIA) represents a well established and appropriate technology among rapid assays because of its low cost and user-friendliness. The antibody-based platform is utilized to detect numerous targets, but it is always hampered by the antibody preparation time, antibody stability, and effect of modification on the antibody. Seeking alternatives to antibodies is an area of active research and is of tremendous importance. Aptamers are receiving increasing attention in lateral flow applications because of a number of important potential performance advantages. We speculate that aptamer-based LFIA may be one of the first platforms for commercial use of aptamer-based diagnosis. This review first gives an introduction to aptamer including the selection process SELEX with its focus on aptamer advantages over antibodies, and then depicts LFIA with its focus on aptamer opportunities in LFIA over antibodies. Furthermore, we summarize the recent advances in the development of aptamer-based lateral flow biosensing assays with the aim to provide a general guide for the design of aptamer-based lateral flow biosensing assays.
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Affiliation(s)
- Ailiang Chen
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing 100081, China.
| | - Shuming Yang
- Institute of Quality Standards and Testing Technology for Agro-products, Key Laboratory of Agro-product Quality and Safety, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Key Laboratory of Agri-food Quality and Safety, Ministry of Agriculture, Beijing 100081, China
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46
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Development of an aptamer-functionalized molecular recognition gating membrane targeting a specific protein on the basis of the aggregation phenomena of DNA–PNIPAM. POLYMER 2015. [DOI: 10.1016/j.polymer.2015.02.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Shastri A, McGregor LM, Liu Y, Harris V, Nan H, Mujica M, Vasquez Y, Bhattacharya A, Ma Y, Aizenberg M, Kuksenok O, Balazs AC, Aizenberg J, He X. An aptamer-functionalized chemomechanically modulated biomolecule catch-and-release system. Nat Chem 2015; 7:447-54. [PMID: 25901824 DOI: 10.1038/nchem.2203] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/12/2015] [Indexed: 12/23/2022]
Abstract
The efficient extraction of (bio)molecules from fluid mixtures is vital for applications ranging from target characterization in (bio)chemistry to environmental analysis and biomedical diagnostics. Inspired by biological processes that seamlessly synchronize the capture, transport and release of biomolecules, we designed a robust chemomechanical sorting system capable of the concerted catch and release of target biomolecules from a solution mixture. The hybrid system is composed of target-specific, reversible binding sites attached to microscopic fins embedded in a responsive hydrogel that moves the cargo between two chemically distinct environments. To demonstrate the utility of the system, we focus on the effective separation of thrombin by synchronizing the pH-dependent binding strength of a thrombin-specific aptamer with volume changes of the pH-responsive hydrogel in a biphasic microfluidic regime, and show a non-destructive separation that has a quantitative sorting efficiency, as well as the system's stability and amenability to multiple solution recycling.
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Affiliation(s)
- Ankita Shastri
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Lynn M McGregor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ya Liu
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Valerie Harris
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Hanqing Nan
- Materials Science and Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Maritza Mujica
- Materials Science and Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA
| | - Yolanda Vasquez
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amitabh Bhattacharya
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Yongting Ma
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Michael Aizenberg
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Olga Kuksenok
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Anna C Balazs
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Joanna Aizenberg
- 1] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA [2] School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA [3] Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts 02138, USA [4] Kavli Institute for Bionano Science and Technology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Ximin He
- 1] Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA [2] Materials Science and Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, USA [3] School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, USA
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48
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Li F, Zhang H, Wang Z, Newbigging AM, Reid MS, Li XF, Le XC. Aptamers facilitating amplified detection of biomolecules. Anal Chem 2014; 87:274-92. [PMID: 25313902 DOI: 10.1021/ac5037236] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Feng Li
- Department of Laboratory Medicine and Pathology, ‡Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada T6G 2G3
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Abstract
In recent years aptamers, synthetic DNA or RNA single-chain oligonucleotides, have been used in various immunological studies to bind specific ligands. Detailed data on the interactions of an RNA aptamer with a human Fc fragment were obtained by X-ray crystallography. The complex formation involves multiple weak interactions that resemble protein-protein interactions. Aptamers specific to cell surface receptors may serve as antagonists or agonists blocking or stimulating cell activities. As aptamers can modify T-cell reactions, they could be useful in the treatment of chronic diseases such as autoimmune and oncological pathologies. In chimeras constructed for the delivery of active substances to defined targets, aptamers specific to surface proteins may be used to transport constructs directed to targets such as tumor cells. Aptamers are also employed as highly specific reagents in immunological assays after being labeled with reporter groups such as fluorescent dyes or following immobilization on insoluble carriers such as membranes or microspheres.
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Affiliation(s)
- Roald Nezlin
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Binding-induced and label-free colorimetric method for protein detection based on autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy. Biosens Bioelectron 2014; 64:572-8. [PMID: 25310491 DOI: 10.1016/j.bios.2014.09.096] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/30/2014] [Accepted: 09/30/2014] [Indexed: 11/21/2022]
Abstract
In this work, a new binding-induced and label-free colorimetric method for protein detection has been developed on the basis of an autonomous assembly of hemin/G-quadruplex DNAzyme amplification strategy. The system consists of two proximity probes carrying two aptamer sequences as recognition elements for target, and two hairpin structures include three-fourths and one-fourth of the G-quadruplex sequences in inactive configuration as functional elements. In the presence of target protein, two proximity probes bind to the protein simultaneously, forming a stable DNA-protein complex. Then the complex triggers an autonomous cross-opening of the two functional hairpin structures, leading to the formation of numerous hemin/G-quadruplex DNAzymes. The resulting DNAzymes catalyze the oxidation of colorless 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(2-)) to the green-colored ABTS(•-) with the presence of H2O2, thus providing the amplified colorimetric detection of target. Using human α-thrombin as the protein target, this binding-induced DNAzyme amplification colorimetric method affords high sensitivity with a detection limit of 1.9 pM. Furthermore, this method might be further extended to sensitive detection of other proteins by simply replacing recognition elements of proximity probes.
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